Prions Take Epigenetics to the ExtremeOctober 28, 2010Yeah, we know that somewhere between the X-games and base-jumping light beer ads, the term “Extreme” got a little played out. But, in their Perspective piece in Science, Randal Halfmann and Susan Lindquist make the case that certain proteins with unique folding properties, called prions, deserve the “extreme” label. Prions are proteins that are stably […]
Pardon the Epigenetic DisruptionOctober 28, 2010One of the great things about stem cells is how they seem to do just about anything. These days, stem cells have more Apps than an iPad, and in the new issue of Science we find one more: using stem cells to screen for “epigenetic disruptors”. The proposed idea is to use the built-in developmental […]
That’s Sweet: Tracking Down 5-hmC with SugarOctober 26, 2010To say researchers have been pretty amped about 5-Hydroxymethylcytosine (5-hmC) this last year would be an understatement. Is this 6th base for real, or is it some kind of intermediate of it’s more abundant cousin 5-mC? So far its low key presence has been detected in embryonic stem cells, brain, and other organs but there […]
Take a Look: NCBI Epigenomics Sample BrowserOctober 26, 2010Our friends at the NCBI clued us in to one of their newest free tools that should prove to be a big help to anyone wanting to sort through next-gen sequencing data from epigenomic studies. NCBI’s new Sample Browser, located on its Epigenomics page, lets users search, access and analyze sequencing data from various publicly […]
Comparative Epigenomics Branches OutOctober 19, 2010When you’re comparing epigenomes, it’s easy to miss the forest for the trees. Because the epigenetic “fruit” on each nucleotide can vary with factors like cell type, differentiation state, and the environment, it’s often tricky to spot patterns on the epigenome-wide scale. In a recent Nature Biotechnology commentary, Aleksandar Milosavlijevic of the NIH Epigenomics Roadmap […]
How to Tame the MethylomeOctober 18, 2010So many ways to analyze genomic DNA methylation, so little time (and money). With so many choices available these days it’s not easy to figure out the best method to use for methylome studies. A new survey of two Nature Biotechnology papers by Stephan Beck from the UK’s University College London puts together the vital […]
Who Says Dnmt1 is Only a Maintenance Methyltransferase?October 5, 2010While investigating the in vitro activity of DNA methyltransferases on annealed oligonucleotide substrates, Australian researchers recently found that murine DNA methyltransferase I will quite happily methylate non-CpG sites in DNA bubbles. Jason Ross and Peter Molloy from the CSIRO, in collaboration with Japanese researchers from the Institute for Protein Research in Osaka, observed a high […]
Do Transcription Factors Occupy All their Binding Motifs in the Genome? Not quite.October 4, 2010A British team of researchers recently decided to take closer look at the role of DNA methylation in conserved consensus motifs. Dr. Roger Foo from the Department of Medicine, University of Cambridge was nice enough to share a bit about their approach that recently published in BMC Genomics (Sept 2010) last week. Transcription factors recognise […]
O-allylhydroxylamine Threatens Bisulfite’s Gold Standard StatusSeptember 23, 2010Let’s get ready to rumble! A new reagent, O-allylhydroxylamine, has entered the ring to challenge bisulfite conversion as the undisputed champion of DNA methylation analysis. In the latest issue of Nucleic Acids Research, chemists from Ludwig-Maximillians University in Germany introduced a new chemical reagent that could be a game-changer for distinguishing between cytosine (C) and […]
Heterogeneous DNA Methylation and Biomarkers: It’s ComplicatedSeptember 23, 2010The state of the economy, global climate change, DNA methylation…These are all complicated issues. Well, we found one well-written review article by Thomas Mikeska, Ida Candiloro, and Alexander Dobrovic at the Peter MacCallum Cancer Centre and the University of Melbourne in Australia that tries to put one of those topics, DNA methylation in perspective, at […]